Microarray technology has been developing quickly since it first appeared in the 1990's (Fodor et al., Science, 251:767–773 (1991)). Now as a representative category of biochip technology, microarray technology has been widely utilized in clinical diagnostics, disease mechanism research, drug discovery, environmental monitoring, functional genomics research etc. (Hacia et al., Nature Genetics, 14: 441–447 (1996); and Heller et al., Proc. Natl. Acad. Sci. USA, 94: 2150–2155 (1997)). Biological probes, such as oligonucleotides, DNA, RNA, peptides, proteins, cells, tissues, are immobilized on the surface of various substrate such as glass, silicon, nylon membrane etc. These probes represent particular information respectively. Sample is added into the reaction well in which the microarray is put to interact with immobilized probes. Sample may be labeled by isotope, fluorescent reagents, chemiluminescent reagents to facilitate the detection. According to different labeling methods, various detection methods can be used, such as confocal fluorescent scanner, low luminescence detector, isotope imager, etc.
To achieve high-throughput parallel analysis, high density microarrays have been developed on which several hundred thousand probes are immobilized. But in many cases, high density and high cost microarrays are not absolutely necessary. Moreover, high density microarrays do not necessarily mean high fidelity of detection signal because different probes on the microarray have subtle distinctions by nature. For example, if probes are DNA molecules, they may have different number of bases or different sequences, both of which contribute to the consequence of varied optimal hybridization conditions. Only under optimal hybridization conditions, mismatch ratio can be reduced to low level to facilitate the generation of accurate hybridization signals. Furthermore, the detection operation is inconvenient for most microarrays as they must be detected one at a time.